from each permutation and each column represents the association between the permuted traits and a specific marker. This matrix was used to adjust the alpha level for multiple comparisons. For example, to calculate the overall p-value for the region, we first calculated the minimum p-value for the observed data, which is 0.009. Then for each permuted data set, we calculated the minimum p-value among the markers, labeling it as pmin,k. The permutation-based p-value for the whole region was estimated as the proportion of the 10,000 permutation runs whose pmin,k was <0.009. Evaluation of the empirical p-value for each marker individually, based on the permutated data sets, resulted in p-values very close to the observed p-values reported in Table 2.
